Subject 47 awakens in his sanatorium to a loudspeaker instructing him to train in various tasks such as scaling obstacles and using firearms, culminating in killing a guard and escaping. The loudspeaker man watches the surveillance satisfied. A year later, 47 is a professional assassin of the International Contract Agency (ICA), briefed by controller Diana Burnwood and is sent around the globe to eliminate four criminal masterminds. In Hong Kong, 47 eliminates Red Dragon triad leader Lee Hong, by first weakening him through orchestrating a gang war between his and a rival triad. 47 is then sent to Colombia where he tracks down and kills drug lord Pablo Belisario Ochoa. In Budapest, 47 assassinates Franz Fuchs, an Austrian terrorist. 47 then infiltrates Rotterdam to kill notorious weapons smuggler Arkadij ""Boris"" Jegorov and his affiliates.
Throughout his missions 47 collects letters written to his targets by the other targets, suggesting that these four are well connected. All four were once part of the French Foreign Legion at about the same time and seem to contact each other regarding an experimental human. The letters also mention a mutual friend among the men, Professor Ort-Meyer. 47 is then alerted by Diana that the same client ordered all of the assassinations, and that the client has ordered one final assassination. 47 is to kill Odon Kovacs, a doctor at a sanatorium in Satu Mare, Romania, the same one from which 47 escaped. When 47 checks in, Ort-Meyer calls the police and is revealed to be the client, as well as the original person which instructed 47 in his escape. Romanian special forces raid the building while 47 kills Kovacs, who is revealed to be a doctor that administered injections to 47.
47 then learns the truth behind his existence. He is the result of a cloning experiment which combined the genetic material of each of his four previous targets, with the addition of Ort-Meyer. The experiments were in the pursuit of creating a flawless human being. Ort-Meyer engineered 47's escape from the asylum in order to test his performance in the outside world and ordered his associates's deaths because they wanted to use the clones for their own purposes. With the help of fellow ICA Agent Smith, who is being held captive and drugged in the building, 47 uncovers a sophisticated lab beneath the hospital. In response Ort-Meyer unleashes a squad of Mr. 48s, an improved and mindlessly loyal series of clones. 47 defeats the clones and confronts Ort-Meyer, who at first mistakes him for another 48. Before Ort-Meyer is able to attack, 47 shoots him. As Ort-Meyer lies dying, mentioning how he could not even recognize his own son, 47 kneels down and forcefully breaks his neck.